3) Preparing and running NGS_DNA pipeline
1) Copy rawdata to rawdata ngs folder
scp –r SEQSTARTDATE_SEQ_RUNTEST_FLOWCELLXX username@yourcluster:${root}/groups/$groupname/${tmpDir}/rawdata/ngs/
2) Create a folder in the generatedscripts folder
mkdir ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
3) Copy samplesheet to generatedscripts folder
scp –r TestRun.csv username@yourcluster:/groups/$groupname/${tmpDir}/generatedscripts/
Note: the name of the folder should be the same as samplesheet (.csv) file
4) Run the generate script
module load NGS_DNA
cd ${root}/groups/$groupname/${tmpDir}/generatedscripts/TestRun
cp $EBROOTNGS_DNA/generate_template.sh .
bash generate_template.sh
cd scripts
Note: If you want to run the pipeline locally, you should change the backend in the CreateInhouseProjects.sh script (this can be done almost at the end of the script where you have something like: sh ${EBROOTMOLGENISMINCOMPUTE}/molgenis_compute.sh search for –b slurm and change it into –b localhost
bash submit.sh
5) Submit jobs
Navigate to jobs folder. The location of the jobs folder will be outputted at the step before this one (step 4).
bash submit.sh